Metacat: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362013-10-03T19:39:23ZEcoinformatics Redmine
Redmine Bug #6117 (Resolved): Reindexing (action=reindex) only works oncehttps://projects.ecoinformatics.org/ecoinfo/issues/61172013-10-03T19:39:23Zben leinfelderleinfelder@nceas.ucsb.eduBug #6101 (Closed): MN.update() fails but modifies revision chainhttps://projects.ecoinformatics.org/ecoinfo/issues/61012013-09-24T23:09:45Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Hello Ben, Chris,</p>
<p>I was trying to update two data and metadata files for some old subtidal data today and ran into a problem. The two new data files updated without issue. The two metadata files did not update with a permissions error…this was the problem we discussed in February and, at that time, Chris manually set up a link between PISCO LDAP data-managers and CILOGON PISCO-data-managers. That link apparently didn’t work today. So, for the second try for the metadata files I used Matt’s suggestion of using the Member Node certificate: ‘urn:node:PISCO.pem’. That didn’t work the first time with a ‘no session has been provided’ error. I figured out that was a file permission error on the cert and fixed that and tried it again. This time the error was ‘the previous identifier has already been made obsolete by <the file I am trying to load> and it didn’t load. It appears the first update call updated the ‘obsoletedBy’ field for the old guid but didn’t load the new metadata. I’m wondering what you think the best way to fix this would be?</p>
<p>The metadata files are:<br /><pre>
pisco_subtidal.70.4 (old) and pisco_subtidal.70.5 (new…not loaded)
pisco_subtidal.80.5 (old) and pisco_subtidal.80.6 (new…not loaded)
</pre></p>
<p>This shows pisco_subtidal.70.4 with obsoletedBy set to pisco_subtidal.70.5 which is not loaded (no object or meta):<br /><a class="external" href="https://data.piscoweb.org/catalog/d1/mn/v1/meta/doi:10.6085/AA/pisco_subtidal.70.4">https://data.piscoweb.org/catalog/d1/mn/v1/meta/doi:10.6085/AA/pisco_subtidal.70.4</a></p>
<pre>
<d1:systemMetadata xmlns:d1="http://ns.dataone.org/service/types/v1">
<serialVersion>2</serialVersion>
<identifier>doi:10.6085/AA/pisco_subtidal.70.4</identifier>
<formatId>eml://ecoinformatics.org/eml-2.0.1</formatId>
<size>27188</size>
<checksum algorithm="MD5">8c17d5bc327f04d6803e5241872fa85c</checksum>
<submitter>uid=cjones,o=PISCO,dc=ecoinformatics,dc=org</submitter>
<rightsHolder>uid=subtidal,o=PISCO,dc=ecoinformatics,dc=org</rightsHolder>
<accessPolicy>
<allow>
<subject>public</subject>
<permission>read</permission>
</allow>
<allow>
<subject>
cn=data-managers,o=PISCOGROUPS,dc=ecoinformatics,dc=org
</subject>
<permission>read</permission>
<permission>write</permission>
<permission>changePermission</permission>
</allow>
</accessPolicy>
<replicationPolicy replicationAllowed="false"/>
<obsoletes>doi:10.6085/AA/pisco_subtidal.70.3</obsoletes>
<obsoletedBy>doi:10.6085/AA/pisco_subtidal.70.5</obsoletedBy>
<archived>false</archived>
<dateUploaded>2007-05-08T23:00:00.000+00:00</dateUploaded>
<dateSysMetadataModified>2013-09-24T17:18:13.620+00:00</dateSysMetadataModified>
<originMemberNode>urn:node:PISCO</originMemberNode>
<authoritativeMemberNode>urn:node:PISCO</authoritativeMemberNode>
<replica>
<replicaMemberNode>urn:node:PISCO</replicaMemberNode>
<replicationStatus>completed</replicationStatus>
<replicaVerified>2012-08-25T00:00:00.000+00:00</replicaVerified>
</replica>
<replica>
<replicaMemberNode>urn:node:CN</replicaMemberNode>
<replicationStatus>completed</replicationStatus>
<replicaVerified>2012-08-25T00:00:00.000+00:00</replicaVerified>
</replica>
</d1:systemMetadata>
</pre>
<p><a class="external" href="https://data.piscoweb.org/catalog/d1/mn/v1/meta/doi:10.6085/AA/pisco_subtidal.70.5">https://data.piscoweb.org/catalog/d1/mn/v1/meta/doi:10.6085/AA/pisco_subtidal.70.5</a><br /><pre>
<error detailCode="1800" errorCode="404" name="NotFound">
<description>
No system metadata could be found for given PID: doi:10.6085/AA/pisco_subtidal.70.5
</description>
</error>
</pre></p> Bug #6100 (Closed): Metacat search does not work for Chinese charactershttps://projects.ecoinformatics.org/ecoinfo/issues/61002013-09-23T17:33:35Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Hi Ben,</p>
<p>We found there is a searching problem on Metacat Home page. We can search Chinese characters correctly on Metacat 1.9.5. but 2.0.3. Does it change the searching way?<br />Thank you for your help.</p>
<p>Best,</p>
<p>Meei-ru</p> Task #6095 (Closed): Pull metacatui from specific taghttps://projects.ecoinformatics.org/ecoinfo/issues/60952013-09-18T22:17:35Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Right now it is pulling the HEAD for the build. Should pull a specific tag.</p> Feature #6092 (Closed): Science Metadata DOIs should point to "view" landing pagehttps://projects.ecoinformatics.org/ecoinfo/issues/60922013-09-16T18:14:04Zben leinfelderleinfelder@nceas.ucsb.edu
<p>We'll use a configurable template for the URI in metacat.properties that will allow us flexibility in determining what the "landing page" for the DOI should be. Will have a property for metadata and for data, defaulting to the /object URI.</p> Feature #6089 (Closed): Remove index_event record when reindex is successfulhttps://projects.ecoinformatics.org/ecoinfo/issues/60892013-09-11T17:13:58Zben leinfelderleinfelder@nceas.ucsb.edu
<p>If manually reindexing a pid that had an error, we should remove the record (if it exists) from the index_event table when the manual reindex completes so that the timed reindex does not attempt to reindex it as well.</p> Bug #6086 (Closed): publish service call fails to authenticate properlyhttps://projects.ecoinformatics.org/ecoinfo/issues/60862013-09-06T23:45:08ZMatt Jonesjones@nceas.ucsb.edu
<p>I was trying to issue a DOI for Sarah Olson's data set tonight via curl on the KNB using the KNB node certificate as my identity. Doing this pointed out two issues, the second of which is definitely a bug.</p>
<p>First error<br />---------<br />I ran this:</p>
<pre>
# curl -X PUT -E /var/metacat/certs/urn_node_KNB.pem http://knb.ecoinformatics.org/knb/d1/mn/v1/publish/solson.11.5
<?xml version="1.0" encoding="UTF-8"?>
<error detailCode="1210" errorCode="401" name="InvalidToken">
<description>No session has been provided</description>
</error>
</pre>
<p>That error is traced back to the beginning of MNodeService.update() where sessions are checked. Looking at ezid, I can see that the DOI was reserved successfully, but then the publish fails doing the update() on the object. I had thought that passing in the client cert was sufficient to identify myself and set up a session, but apparently not. Any thoughts on why this didn't work, and what is needed to successfully log in via curl? There may not be a bug here, but rather me using curl incorrectly. Or maybe it should work.</p>
<p>Second error<br />-----------<br />Also, it seems that the EZID mint() call worked even though I wasn't authenticated on metacat, so I tried the same call again without a certificate at all:</p>
<pre>
# curl -X PUT http://knb.ecoinformatics.org/knb/d1/mn/v1/publish/solson.11.5
</pre>
<p>and I got the same error. The new DOI is still reserved on the EZID system despite not being authenticated in Metacat, so there seems to be a bug here in not checking the session before contacting EZID to mint() the identifier.</p> Bug #6085 (Closed): SQL error when inserting EML beta2 access documenthttps://projects.ecoinformatics.org/ecoinfo/issues/60852013-09-06T21:23:41Zben leinfelderleinfelder@nceas.ucsb.edu
<p>I was showing Lauren how to use the perl lib to transfer test content from one Metacat to her localhost and we got this error for old EML beta6 access docs" <br /><pre>
error msg: AccessControlList.insertPermissions(): ERROR: column "docid" of relation "xml_access" does not exist
</pre></p>
<p>This was an oversight when we moved to using guid instead of docid for the xml_access table.</p>
<p>I am not terribly worried about this since those documents really aren't supported any more, but I would like the SQL to be correct nonetheless.</p>
<p>Example file: obfs.147.2</p> Story #6082 (Closed): Rename knb.war to ???.warhttps://projects.ecoinformatics.org/ecoinfo/issues/60822013-09-06T19:41:54Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Possible names (please add more suggestions):<br />-metacat.war (would make <hostname>/metacat/metacat for the Metacat servlet which I think is very confusing)<br />-catalog.war<br />-repository.war<br />-m.war<br />-mc.war</p> Task #6081 (Closed): Build metacatui.war in Metacat bundlehttps://projects.ecoinformatics.org/ecoinfo/issues/60812013-09-06T19:36:52Zben leinfelderleinfelder@nceas.ucsb.eduTask #6069 (Closed): Pull metacatui from public Git repo into Metacathttps://projects.ecoinformatics.org/ecoinfo/issues/60692013-09-06T00:11:00Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Since the original nceas staff repo for datadepot is protected (even for reading) we need to push the release tags to our public github repo clone and pull from there during the metacat build.</p>
<p><a class="external" href="https://github.com/NCEAS/metacatui.git">https://github.com/NCEAS/metacatui.git</a></p> Task #6066 (Closed): Add email verification for new accountshttps://projects.ecoinformatics.org/ecoinfo/issues/60662013-09-05T23:43:09Zben leinfelderleinfelder@nceas.ucsb.edu
<p>We should send a temporary link to activate an account using on a randomly-generated key for their provisional account registration.</p>
<p>We should also remember to clear out the entries that have not been activated after X number of hours (maybe start with 36 hours?). Would be great if this were automated. Maybe ldapweb.cgi could just clear the old ones out whenever it is activated - won't necessarily be that often, but it will take care of old entries. Not a huge risk because the entries in the tmp subtree can't do anything.</p> Bug #6061 (Closed): Ensure that all packages from metacat API have resource maphttps://projects.ecoinformatics.org/ecoinfo/issues/60612013-09-02T18:03:05ZMatt Jonesjones@nceas.ucsb.edu
<p>Data package downloads no longer have data files in them, even when the data are present in Metacat via an upload from Morpho. This is probably because packages uploaded via the Metacat API (deprecated) do not have an attached resource map file. We need to ensure that these resource map files are systematically included because, without them, the downloads for packages do not include the data. We have gotten several complaints about this since the new MetacatUI interface wen public. TO close this bug:</p>
<p>1) Create a mechanism to create resource maps for all packages as they are uploaded using the Metacat API. This may need to run after all components of the package have been uploaded.<br />2) Ensure that the mechanism creates resource maps for older packages that were uploaded using the Metacat API before the present time</p> Bug #6054 (Closed): dataPackage.xxxx.zip BagIt package is unzipped as "bag"https://projects.ecoinformatics.org/ecoinfo/issues/60542013-08-22T22:38:44Zben leinfelderleinfelder@nceas.ucsb.edu
<p>It should be "dataPackage" or a mangled version of the PID</p> Bug #5647 (Closed): Lack of access rights for "previous" datafile prevent savinghttps://projects.ecoinformatics.org/ecoinfo/issues/56472012-08-06T22:56:22Zben leinfelderleinfelder@nceas.ucsb.edu
<p>I believe this problem was the culprit for [some of] James Wilkins' problems saving datapackages to Metacat.<br />Here's the scenario:<br />1. userA inserts EML (meta.1.1) and data (data.1.1) with access rules to allow ALL for userB.<br />2. userA edits EML and edits data file but it contains invalid XML<br />3. userA saves data file (data.1.2) the EML file (meta.1.2), but it fails on the EML parsing.<br />At this point, the server has data.1.1, data.1.2 and meta.1.1 but no access rules for data.1.2 because they were never parsed from the failed meta.1.2 document.<br />4. userB fixes the parsing error in the EML file and attempts to save<br />5. userB cannot save because userB does not have access to the data.1.2 file</p>